A multimethod approach to analyse the dietary composition of the Baltic grey seal (Halichoerus grypus) in the southern Baltic

Baltic grey seals (Halichoerus grypus) returned to the Southern Baltic Sea in the early 2000s, and in 2021 more than 40,000 were counted in the Baltic Sea, with about 10 % of the population found in the southern Baltic. As top predators, grey seals compete to some extent with coastal fisheries for the same resource. Estimation of total consumption of key fish species by grey seals is hampered by the low natural abundance of some species such as northern pike (Esox lucius) as well as high mobility of seals, which move among inner and outer coastal waters where the fish communities differ. Moreover, grey seals are known to feed on soft tissue of large-bodied species such as pike or marine mammals. Therefore, hard parts of those species may not be detectable with morphological analyses. We anticipated a better understanding of the grey seal diet composition by including genetic analyses. In this study, morphological and genetic methods are combined to compare the approach of these two methods in connection to the estimation of the diet composition of Baltic grey seals. Samples were collected during necropsies within the marine mammal stranding network of the German Oceanographic Museum in Mecklenburg-Western Pomerania (Germany). In total, 104 intestine- and 23 stomach-content samples were taken and following DNA was extracted. The mitochondrial 16S rRNA gene was targeted for DNA metabarcoding, using a combination of existing primers and newly designed primers that cover the expected local diet of grey seals, for 26 grey seals. For direct comparison, 7 whole intestines and stomachs were analysed morphologically and genetically. Additionally, samples of 32 seals of stomach and intestines were analysed morphologically separately to investigate the results of this method. With morphological analysis, herring, cod and round goby were found to important prey species of grey seals. Prey-fish size and species was related to seal size. Genetic analysis detected 40% more species than morphological analysis, but was subject to contamination in some negative controls, thus conclusions to be drawn are limited. Nonetheless, herring, sculpin, and roach were found to be important prey species. DNA concentration decreased with increasing decomposition state, which may influence the detection of prey species with this method. There were no significant differences in prey abundance among different areas along the coast of Mecklenburg-Western Pomerania, or in different years and seasons (quarters). Gamma diversity revealed a high diversity in prey-fish community, with no single species overly dominating the diet.